Toward High-Throughput Genotyping: Dynamic and Automatic Software for Manipulating Large-Scale Genotype Data Using Fluorescently Labeled Dinucleotide Markers

Li, Jin Long; Deng, Hong‐Wen; Lai, Dong; Xu, Fusheng; Chen, Jian; Gao, Guimin; Recker, Robert R.; Deng, Hong Wen

doi:10.1101/gr.159701

Cited by 61 publications

(36 citation statements)

References 19 publications

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“…The allele binning was carried out using all the fragment sizes obtained in all the samples and all the repetitions analysed. Two approaches were used: frequency histograms for each marker and the plotting technique [22] based in sorted allele sizes.…”

Section: Allele Binning and Data Analysismentioning

confidence: 99%

Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

et al. 2008

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-In order to protect the legitimate interests of the poplar breeders, growers and industries, we have developed a reliable and affordable certification tool for commercial poplars in Spain. We have carried out a genetic description of the 28 commercial clones of the current Spanish National Catalogue using 10 microsatellite molecular markers (SSR). The results clearly show that in the Spanish National Catalogue there are labelling mistakes including synonymies, supported by a combined probability of identity (PI) of 1.18 × 10 −9 . We have also demonstrate that it is possible to identify all the different clones (genotypes) with only three microsatellites, that show a combined probability of identity of 2.4 × 10 −4 , and we have optimised the protocols to reduce the time and the economical costs of the analysis. This SSR-based tool could be incorporated in the current certification protocols, to avoid duplication of accessions and identification mistakes.commercial poplar clone / microsatellite / identification / Spanish national catalogue Résumé -Développement de marqueurs microsatellites pour l'identification et la certification des clones commerciaux de peuplier en Espagne. Dans le but de protéger les intérêts légitimes des cultivateurs, des sélectionneurs et des industriels de la populiculture, nous avons mis au point un outil de certification fiable et accessible pour les clones de peupliers commerciaux en Espagne. Nous avons fait une description génétique des 28 clones commerciaux de l'actuel catalogue national espagnol en utilisant 10 marqueurs moléculaires microsatellites (SSR). Les résultats obtenus indiquent clairement que ce catalogue contient des erreurs d'identification, dont des clones synonymes, soutenues par une probabilité combinée d'identité (PI) de 1.18 × 10 −9 . Nous avons également démontré qu'il est possible d'identifier tous les génotypes différents avec 3 microsatellites, qui montrent une probabilité combinée d'identité de 2.4 × 10 −4 , et nous avons optimisé les protocoles afin de réduire le temps et le coût de l'analyse. Cet outil fondé sur les SSR pourrait être intégré dans les protocoles actuels de certification afin d'éviter la duplication des matériaux et les erreurs d'identification.clone commercial de peuplier / microsatellite / identification / catalogue national espagnol

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Section: Allele Binning and Data Analysismentioning

confidence: 99%

Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

et al. 2008

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“…Because the distribution of allele frequencies at most microsatellite loci was normal, the analysis was based on the repeat number of main allele for each locus. Dinucleotide repeats are reported to be most common and polymorphic in plants (Morgante & Olivieri 1993;Li et al 2001).…”

Section: Discussionmentioning

confidence: 99%

Study of the genetic diversity of Korean, Chinese and Japanese landraces of barley (Hordeum vulgare L.) using microsatellites

Park¹,

Dong

Baek

et al. 2011

Biodiversity: Research and Conservation

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Barley (Hordeum vulgare L.) is one of important winter cereals in the world and has been the subject of numerous genetic investigations. Studies of its genetic diversity based on germplasm have a significant impact on crop breeding and conservation of genetic resources. This study was conducted to reveal the genetic diversity in barley landraces from Korean, Chinese and Japanese populations and evaluate the discrimination ability of SSR markers, distributed uniformly throughout the barley genome. Seven SSR primers were used to screen a set of 737 diverse barley landraces from Korea, China and Japan. The observed number of alleles per locus (Na), the effective number of alleles (Ne), and the mean gene diversity (He) were 11.14, 3.6245 and 0.7048, respectively. The number of alleles per locus was highest in Chinese landraces (8.9 alleles), followed by Korean (8.6) and Japanese (6.4). In this regard, HVKASI primer may be useful to distinguish Japanese landraces from others, as this unique allele was only detected at 175 bp in Japanese landraces. The average value of genetic distance was D=0.935. The largest genetic distance (D=1.209) among the three regional (representing each country in general) populations was found between Korean and Japanese populations. Based on the UPGMA dendrogram, four major groups can be distinguished at the similarity value of 0.43. The scatter plot showed overlapping in the central part amongst 3 groups of barley landraces. SSR markers are a powerful tool to examine functional diversity. Rich barley gene pool can be very useful for meeting current and future challenges in barley raising.

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“…Several groups have proposed improved protocols for binning alleles (Ghosh et al 1997;Idury and Cardon 1997;Li et al 2001).…”

Section: Genome Research 433mentioning

confidence: 99%

A Tale of Two Genotypes: Consistency between Two High-Throughput Genotyping Centers

Weeks¹,

Conley²,

Ferrell³

et al. 2002

Genome Res.

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Multiple genome-wide scans involving sib-pairs or limited pedigrees have been extensively used for a wide number of complex genetic conditions. Comparing data from two or more scans, as well as combining data, require an understanding of the sources of genotyping errors and data discrepancies. We have conducted two genome-wide scans for age-related maculopathy using the Center for Inherited Disease Research (CIDR) and the Mammalian Genotyping Service (MGS). Thirty individuals were typed in common, in order to allow for the alignment of alleles and comparison of the data sets. The analysis of these 8914 genotypes distributed over 321 markers in common demonstrated excellent agreement between these two laboratories, which have low rates of internal errors. Under the assumption that within each genotype, the smaller MGS allele should correspond to the smaller CIDR allele, the alleles align well between the two centers, with only a small fraction (less than 0.65%) of the aligned alleles showing large differences in sizes. However, since called allele sizes are integer "labels" which may not directly reflect the true underlying allele sizes, it is important to carefully prepare in advance if one wishes to merge data from different laboratories. In particular, it would not suffice to attempt to align alleles by typing only one or two controls in common. Fortunately, for the purposes of linkage analysis, one can avoid merging difficulties by simply carrying out linkage analyses using laboratory-specific allele labels and allele frequencies for each laboratory-specific subset of the data.As genotyping has become less expensive, it has become common to attempt to map disease genes via genome-wide scans (Weeks and Lathrop 1995). In fact, large-scale genotyping centers have been established to facilitate this process throughout the world. In the United States, the National Institutes of Health (NIH) have funded two prominent genotyping centers: the Mammalian Genotyping Service (MGS), led by Dr. James Weber and funded by the National Heart, Lung, and Blood Institute; and the Center for Inherited Disease Research (CIDR), led by Dr. David Valle and funded by 11 NIH Institutes. At these Centers, millions of genotypes are being generated per year: In 1999, MGS generated 5.54 million genotypes and CIDR generated approximately 1.2 million genotypes. These two centers, which both use multiallelic short tandem repeat (STR) markers, have extensive experience, and report very small internal error rates. MGS reports an average genotype error rate of 0.7%, based on blindly typing Centre d'Étude du Polymorphisme Humain (CEPH) family DNA samples in duplicate or triplicate on different gels (Weber and Broman 2001); note that the allele error rate is approximately 60% of the genotype error rate (as usually one of the two alleles is correct for most incorrect genotypes). CIDR reports an error rate of 0.18% based on more than 2 million genotypes; these error rates are based on four blind duplicates of investigator-supplied samples per 96-lan...

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Toward High-Throughput Genotyping: Dynamic and Automatic Software for Manipulating Large-Scale Genotype Data Using Fluorescently Labeled Dinucleotide Markers

Cited by 61 publications

References 19 publications

Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

Study of the genetic diversity of Korean, Chinese and Japanese landraces of barley (Hordeum vulgare L.) using microsatellites

A Tale of Two Genotypes: Consistency between Two High-Throughput Genotyping Centers

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